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Genomic and epigenomic heterogeneity of hepatocellular carcinoma. (Cancer Res, Feb 2017)

Lin DC1, Mayakonda A2, Dinh HQ3, Huang P4, Lin L5, Liu X6, Ding LW7, Wang J8, Berman B9, Song E10, Yin D5, Koeffler HP11.

1 Cedars-Sinai Medical Center
2 National Cancer Institute,Cancer Science Institute,, National University of Singapore.
3 Cedars-Sinai Medical Center.
4 Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University.
5 Key Laboratory of Malignant Tumor Gene Regulation, Sun Yat-Sen Memorial Hospital.
6 Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences.
7 Cancer Science Institute of Singapore, National University of Singapore.
8 Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital.
9 Epigenome Center, University of Southern California.
10 Sun Yst-sen Memorial Hospital, Sun Yst-sen university.
11 Department of Medicine, Cedars-Sinai Medical Center.

Abstract
Understanding the intratumoral heterogeneity of hepatocellular carcinoma (HCC) is instructive for developing personalized therapy and identifying molecular biomarkers. Here we applied whole-exome sequencing to 69 samples from 11 patients to resolve the genetic architecture of subclonal diversification. Spatial genomic diversity was found in all 11 HCC cases, with 29% of driver mutations being heterogeneous, including TERT, ARID1A, NOTCH2, and STAG2. Similar with other cancer types, TP53 mutations were always shared between all tumor regions i.e. located on the “trunk” of the evolutionary tree. In addition, we found that variants within several drug targets such as KIT, SYK and PIK3CA were mutated in a fully clonal manner, indicating their therapeutic potentials for HCC. Temporal dissection of mutational signatures suggested that mutagenic processes associated with exposure to aristolochic acid and aflatoxin might play a more important role in early, as opposed to late, stages of HCC development. Moreover, we observed extensive intratumoral epigenetic heterogeneity in HCC based on multiple independent analytical methods and showed that intratumoral methylation heterogeneity might play important roles in the biology of HCC cells. Our results also demonstrated prominent heterogeneity of intratumoral methylation even in a stable HCC genome. Together, these findings highlight widespread intratumoral heterogeneity at both the genomic and epigenomic levels in HCC and provide an important molecular foundation for better understanding the pathogenesis of this malignancy.

Copyright ©2017, American Association for Cancer Research.

PMID: 28302680